Targeted sequencing of cell-free DNA for monitoring of prostate cancer progression

用于监测前列腺癌进展的游离 DNA 靶向测序

基本信息

批准号：
10687121
负责人：
Jace Webster
金额：
$ 3.36万
依托单位：
WASHINGTON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-01 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10687121
关键词：
Address Affect African American population American Androgen Receptor BRCA2 gene Bioinformatics Biological Assay Biological Markers Biopsy Blood Cancer Biology Cancer Patient Castration Caucasians Cells Cellular Assay Clinical Computer software Copy Number Polymorphism Country Custom DNA analysis DNA sequencing Data Development Diagnosis Disease Disease Progression Disease Resistance Enhancers Environment Ethnic Origin Exhibits Genes Genetic Genomics Goals Human Impairment Malignant neoplasm of prostate Mentorship Metastatic Prostate Cancer Methods Molecular Monitor Mutate Mutation Neoplasm Circulating Cells Neoplasm Metastasis Newly Diagnosed Outcome Paper Patient Care Patients Performance Pharmaceutical Preparations Population Publications Publishing RNA Splicing Refractory Reproducibility Research Research Personnel Resistance Running Sampling Single Nucleotide Polymorphism Software Tools Standardization Stereotyping Stratification TP53 gene Testing Time Training Tumor Biology Underrepresented Populations Universities Validation Variant Washington Work abiraterone androgen deprivation therapy anticancer research bioinformatics tool career castration resistant prostate cancer cell free DNA chemotherapy clinical application clinical translation clinically relevant cohort density detection assay effective therapy enzalutamide exome sequencing gene panel genome sequencing high risk improved individualized medicine knowledge translation liquid biopsy men molecular marker non-invasive monitor open source patient stratification programs prospective prostate cancer progression skills software development standard care standard of care targeted sequencing taxane tool transcriptome sequencing translational impact user-friendly variant detection whole genome

项目摘要

PROJECT SUMMARY / ABSTRACT Prostate cancer (PCa) results in more than 160,000 diagnoses in the US each year with essentially all patients eventually progressing to metastatic castration-resistant prostate cancer (mCRPC), the more lethal form of the disease. Early stratification of mCRPC patients is critical since 20-40% exhibit primary resistance to first-line treatments and those with resistance have a median survival of only 5.5 months. The standard-of-care circulating tumor cell assay (monitoring the AR-V7 splice variant) highlights the potential for a non-invasive method for monitoring PCa disease progression, but it gives 80-90% of patients a false-negative and has only ~3% sensitivity when used pre-treatment. The long-term objective of this proposal is to investigate the potential of a cell-free DNA (cfDNA)-based assay for mCRPC patient stratification to improve upon the current standard-of-care. To address this, the current proposal leverages our published cfDNA assay that monitors the recently discovered tandem duplication of an enhancer region upstream of the androgen receptor (AR), additional AR mutations, and 83 additional genes commonly mutated in mCRPC. Our gene panel and cfDNA analysis method (EnhanceAR-Seq) outperformed the current standard-of-care in a prospectively collected cohort of mCRPC patients. While this highlights the clinical utility of monitoring SVs non-invasively, no automated pipelines exist for SV calling using targeted cfDNA assays. Copy number variation (CNV) and SV analysis of cfDNA using a targeted sequencing approach requires specific considerations not accounted for in traditional pipelines, such as the influence of probe density on read depth. This in turn results in researchers developing custom scripts and parameters for running multiple tools for analysis of different variant classes (SV, CNV, single nucleotide variants) and ultimately impairing the reproducibility of clinically relevant work. This serves as a strong rationale for the following aims to (1) develop a standardized and robust unified pipeline for somatic variant calling of all classes using cfDNA and (2) assess the clinical utility of EnhanceAR-Seq across (a) an independent validation mCRPC patient cohort, (b) across ethnicities and (c) in an earlier clinical setting. The research will be completed with mentorship from Dr. Christopher Maher and through the Human and Statistical Genetics program at Washington University, one of the top ranked genetics programs in the country. The Maher lab is an ideal environment for this project given their extensive bioinformatics, software development, structural variation, genomics, and prostate cancer biology expertise. Training will focus on (1) developing computational skills through software development and the application of bioinformatics tools, (2) improving knowledge of translational tumor biology, and (3) professional development, all of which will support the goal of a career in cancer research. This study will have an overall impact on the field by providing a standardized and reproducible method for variant calling with cfDNA in a non-invasive assay, which will be broadly applicable beyond PCa. Long term, this research has enormous potential for clinical translation by improving PCa patient care.

项目摘要/摘要美国有超过 160,000 例前列腺癌 (PCa) 确诊病例每年，基本上所有患者最终都会进展为转移性去势抵抗性前列腺癌 (mCRPC)，该疾病更致命的形式。 mCRPC 患者的早期分层至关重要，因为 20-40% 对一线治疗表现出主要耐药性，而具有耐药性的患者的中位生存期仅为 5.5 几个月。标准护理循环肿瘤细胞测定（监测 AR-V7 剪接变体）强调了监测 PCa 疾病进展的非侵入性方法具有潜力，但它为 80-90% 的患者提供了假阴性，并且在治疗前使用时敏感性仅为约 3%。本提案的长期目标旨在研究基于游离 DNA (cfDNA) 的检测方法对 mCRPC 患者分层的潜力，以改善根据目前的护理标准。为了解决这个问题，当前的提案利用了我们发布的 cfDNA 检测监测最近发现的雄激素上游增强子区域的串联重复受体 (AR)、其他 AR 突变以及 mCRPC 中常见的 83 个其他基因。我们的基因组 cfDNA 分析方法 (EnhanceAR-Seq) 在前瞻性方面优于当前的护理标准收集 mCRPC 患者队列。虽然这凸显了非侵入性监测 SV 的临床实用性，但没有存在使用靶向 cfDNA 检测进行 SV 调用的自动化流程。拷贝数变异 (CNV) 和 SV 使用靶向测序方法分析 cfDNA 需要具体考虑因素，但未在传统的管道，例如探针密度对读取深度的影响。这反过来又导致研究人员开发自定义脚本和参数来运行多个工具来分析不同的变体类（SV、 CNV，单核苷酸变异）并最终损害临床相关工作的可重复性。这为实现以下目标提供了强有力的理由：(1) 开发标准化且强大的统一管道使用 cfDNA 对所有类别进行体细胞变异检出，并 (2) 评估 EnhanceAR-Seq 的临床效用 (a) 一个独立验证的 mCRPC 患者队列，(b) 跨种族，(c) 在早期临床环境中。这研究将在 Christopher Maher 博士的指导下并通过人类和统计研究所完成华盛顿大学的遗传学项目是全国排名最高的遗传学项目之一。马赫实验室是该项目的理想环境，因为其广泛的生物信息学、软件开发、结构变异、基因组学和前列腺癌生物学专业知识。培训将侧重于 (1) 开发计算能力通过软件开发和生物信息学工具的应用来提高技能，（2）提高知识转化肿瘤生物学，以及（3）专业发展，所有这些都将支持职业目标癌症研究。这项研究将通过提供标准化且可重复的方法对该领域产生整体影响。在非侵入性检测中使用 cfDNA 进行变异识别的方法，该方法将广泛适用于 PCa 之外的领域。从长远来看，这项研究通过改善前列腺癌患者护理而具有巨大的临床转化潜力。